#21 Add frontend filters

cmd/mb3server/src/api-impl.go

@@ -2,6 +2,7 @@ package mb3server
 
 import (
  "github.com/MassBank/MassBank3/pkg/database"
+ "github.com/MassBank/MassBank3/pkg/massbank"
  "log"
  "os"
 )
@@ -34,7 +35,11 @@ func initDB() error {
  return err
  }
  }
- return db.Ping()
+ err := db.Ping()
+ if err != nil {
+ db = nil
+ }
+ return err
 
 }
 
@@ -82,40 +87,67 @@ func GetBrowseOptions() (*BrowseOptions, error) {
  Count: int32(val.Count),
  })
  }
- for _, val := range vals.CompoundStart {
- result.CompoundStart = append(result.CompoundStart, StringCountInner{
- Value: val.Val,
- Count: int32(val.Count),
- })
- }
 
  return &result, nil
 }
 
-func GetRecords(limit int32, page int32) (*SearchResult, error) {
+func GetRecords(limit int32, page int32, contributor string, instrumentType []string, msType []string, ionMode string) (*SearchResult, error) {
  if limit <= 0 {
  limit = 20
  }
  if page <= 0 {
  page = 1
  }
+
+ msTypeLokal := &[]massbank.MsType{}
+ for _, t := range msType {
+ switch t {
+ case "MS":
+ *msTypeLokal = append(*msTypeLokal, massbank.MS)
+ case "MS2":
+ *msTypeLokal = append(*msTypeLokal, massbank.MS2)
+ case "MS3":
+ *msTypeLokal = append(*msTypeLokal, massbank.MS3)
+ case "MS4":
+ *msTypeLokal = append(*msTypeLokal, massbank.MS4)
+ }
+ }
+
+ if len(*msTypeLokal) == 0 {
+ msTypeLokal = nil
+ }
+
+ var ionModeLokal massbank.IonMode = massbank.ANY
+ switch ionMode {
+ case "POSITIVE":
+ ionModeLokal = massbank.POSITIVE
+ case "NEGATIVE":
+ ionModeLokal = massbank.NEGATIVE
+ }
+ log.Println(ionModeLokal)
+ it := &instrumentType
+ if len(*it) == 0 {
+ it = nil
+ }
+
  var offset = (page - 1) * limit
  if err := initDB(); err != nil {
  return nil, err
  }
+
  var filters = database.Filters{
  InstrumentType: nil,
  Splash: "",
- MsType: nil,
- IonMode: "",
+ MsType: msTypeLokal,
+ IonMode: ionModeLokal,
  CompoundName: "",
  Mass: nil,
  MassEpsilon: nil,
  Formula: "",
  Peaks: nil,
  PeakDifferences: nil,
  InchiKey: "",
- Contributor: "",
+ Contributor: contributor,
  IntensityCutoff: nil,
  Limit: int64(limit),
  Offset: int64(offset),

cmd/mb3server/src/api_default_service.go

@@ -70,7 +70,7 @@ func (s *DefaultApiService) GetRecord(ctx context.Context, accession string) (Im
 
 // GetRecords - Get a list of records
 func (s *DefaultApiService) GetRecords(ctx context.Context, instrumentType []string, splash string, msType []string, ionMode string, compoundName string, exactMass string, massTolerance float64, formula string, peaks []string, intensity int32, peakDifferences []string, peakList []string, limit int32, page int32, intensityCutoff int32, inchiKey string, contributor string) (ImplResponse, error) {
- result, err := GetRecords(limit, page)
+ result, err := GetRecords(limit, page, contributor, instrumentType, msType, ionMode)
  if err != nil {
  return Response(http.StatusInternalServerError, nil), errors.New("Could not get results")
  }

pkg/database/mongodb.go

@@ -56,26 +56,6 @@ func (db *Mb3MongoDB) GetUniqueValues(filters Filters) (MB3Values, error) {
  var query = `
 [
  { "$facet": {
- "CompoundStart": [
- { "$project": { "compound.names": 1}},
- { "$unwind": "$compound.names" },
- {"$group": {
- "_id": {"$substr": [ {"$trim": { "input": {"$toUpper":"$compound.names"}, "chars": "()+-[]{}/? ,"}},0,1]},
- "Count": {"$sum": 1}
- }},
- {
- "$project": {
- "_id": 0,
- "Val": "$_id",
- "Count": 1
- }
- },
- {
- "$sort": {
- "Val": 1
- }
- }
- ],
  "Contributor": [
  {
  "$project": { "_id": 0, "cont": {"$arrayElemAt":[ {"$split": [ "$accession","-"]}, 1]} }
@@ -359,6 +339,13 @@ func (db *Mb3MongoDB) Ping() error {
  timeout, _ := time.ParseDuration(MongoConnectTimeout)
  ctx, cancel := context.WithTimeout(context.Background(), timeout)
  defer cancel()
+ if db.database == nil {
+ return errors.New("Database not connected")
+ }
+ client := db.database.Client()
+ if client == nil {
+ return errors.New("Database not connected")
+ }
  return db.database.Client().Ping(ctx, nil)
 }
 

web-frontend/src/lib/components/FilterBox.svelte

@@ -1,19 +1,20 @@
 <script>
  export let group;
- export let val;
- let values= []
+ export let values;
+ export let result= [];
 </script>
 
+{#each values as v}
 <div class="filteroption">
 <label>
- <input type=checkbox bind:group={values} name={group} value={val}>
- <slot />
+ <input type=checkbox bind:group={result} name={group} value={v.value}>
+ {v.value} ({v.count}}
 </label>
 </div>
-
+{/each}
 <style>
  .filteroption {
  font-size: 0.8em;
  padding: 0 0.5em;
  }
-</style>
+</style>

web-frontend/src/lib/components/Pagination.svelte

@@ -25,6 +25,9 @@
 <slot></slot>
 
 <style>
+ .pagination {
+ padding: 1em;
+ }
  .current-page {
  font-size: 1.2em;
  font-weight: bold;

web-frontend/src/routes/contents/+page.svelte

@@ -24,6 +24,11 @@
  async function getResults(page) {
  let url = new URL("/v1/records",base)
  url.searchParams.append('page',page.toString())
+ contribuors.forEach(element => url.searchParams.append('contributor',element))
+ msType.forEach(element => url.searchParams.append('ms_type',element))
+ instrumentType.forEach(element => url.searchParams.append('instrument_type',element))
+ ionMode.forEach(element => url.searchParams.append('ion-mode',element))
+
  console.log(url)
  let resp = await fetch(url)
  let jsonData = await resp.json();
@@ -37,10 +42,14 @@
  }
  }
 
- $: base = data.baseurl;
+ let contribuors = [];
+ let msType = [];
+ let instrumentType = [];
+ let ionMode = [];
+ $: base = data.baseurl
 </script>
-
-{page}
+{base}
+{contribuors}
 <div class="pure-g">
  <div class="pure-u-1-5">
  {#await getFilters(base)}
@@ -49,25 +58,13 @@
  <div class="card">
  <h2>Filters</h2>
  <h3>Contributor</h3>
- {#each filters.contributor as t}
- <FilterButton group="cont" val={t.value}>{t.value} ({t.count})</FilterButton>
- {/each}
+ <FilterButton bind:result={contribuors} group="cont" values={filters.contributor}></FilterButton>
  <h3>Instrument Type</h3>
- {#each filters.instrument_type as t}
- <FilterButton group="insttype" val={t.value}>{t.value} ({t.count})</FilterButton>
- {/each}
+ <FilterButton bind:result={instrumentType} group="itype" values={filters.instrument_type}></FilterButton>
  <h3>MS Type</h3>
- {#each filters.ms_type as t}
- <FilterButton group="mstype" val={t.value}>{t.value} ({t.count})</FilterButton>
- {/each}
+ <FilterButton bind:result={msType} group="mstype" values={filters.ms_type}></FilterButton>
  <h3>Ion Mode</h3>
- {#each filters.ion_mode as t}
- <FilterButton group="ionmode" val={t.value}>{t.value} ({t.count})</FilterButton>
- {/each}
- <h3>Compound Start</h3>
- {#each filters.compound_start as t}
- <FilterButton group="compoundstart" val={t.value}>{t.value} ({t.count})</FilterButton>
- {/each}
+ <FilterButton bind:result={ionMode} group="imode" values={filters.ion_mode}></FilterButton>
  </div>
  {:catch error}
  <div class="error">Error during Filter loading</div>